leonarski_f
a9d5367013
Build Packages / Create release (push) Successful in 26s
Build Packages / Build documentation (push) Successful in 1m43s
Build Packages / build:portable:macos-arm64:nocuda (push) Successful in 5m7s
Build Packages / build:portable:linux-x86_64:nocuda (push) Successful in 11m48s
Build Packages / build:rugnux:linux-aarch64:cuda (push) Successful in 7m22s
Build Packages / build:portable:linux-x86_64:cuda (push) Successful in 12m24s
Build Packages / HDF5 consumer tests (DIALS, XDS) (push) Successful in 25m30s
Build Packages / build:portable:windows-x86_64:nocuda (push) Successful in 25m29s
Build Packages / build:portable:windows-x86_64:cuda (push) Successful in 29m41s
Build Packages / build:jfjoch:ubuntu2204:nocuda (push) Successful in 21m44s
Build Packages / build:jfjoch:rocky8:nocuda (push) Successful in 24m41s
Build Packages / build:jfjoch:rocky9:nocuda (push) Successful in 26m9s
Build Packages / build:jfjoch:ubuntu2404:nocuda (push) Successful in 26m3s
Build Packages / build:jfjoch:rocky8:cuda-sls9 (push) Successful in 28m28s
Build Packages / Generate python client (push) Successful in 27s
Build Packages / build:jfjoch:rocky9:cuda-sls9 (push) Successful in 31m16s
Build Packages / build:jfjoch:ubuntu2204:cuda (push) Successful in 20m44s
Build Packages / build:jfjoch:rocky8:cuda (push) Successful in 26m27s
Build Packages / build:jfjoch:ubuntu2404:cuda (push) Successful in 22m52s
Build Packages / build:jfjoch:rocky9:cuda (push) Successful in 27m44s
Build Packages / Unit tests (push) Successful in 1h46m55s
Build Packages / Validation Battery (push) Successful in 52m50s
* Rugnux: Several rotation sweeps of one crystal are merged as one dataset (`rugnux a_master.h5 b_master.h5`), on a common indexing and cell, with a non-isomorphous sweep left out and reported; `--sweeps separate` processes each sweep on its own. Bruker `.sfrm` frames and imgCIF files with a full goniometer axis chain are read. * Rugnux: More robust rotation processing - a retry with a more sensitive spot finder when no lattice is found, a self-consistent detector distance, long axes and doubled cells tested as hypotheses, a `-C` supercell multiple stepped down, and each ice ring merged, down-weighted or rejected on its own. * Rugnux: Serial stills are merged with a partiality-aware error model, reported as `ERROR_MODEL_A/B/C` with no ISa or R_merge/R_meas/R_pim; runs without `-S` have an overall intensity scale about 0.86-0.88 times that of earlier versions, with unchanged statistics. A second crystal form is left out of the merge and reported, the indexing ambiguity is resolved more reliably, and `--model` no longer influences processing. * Rugnux: The reported CC1/2 is the standard unweighted one, which can be lower than before on sweeps with weak frames; ISa comes with a 95% interval (`ISA_LOW`/`ISA_HIGH`). * Rugnux: Model refinement adds anisotropic/TLS, local NCS and twin refinement where R-free supports them; building waters and relabelling ions is now off by default (`--refine-solvent` turns it on). * NXmx: A detector of several modules is written as `module_0` ... `module_N` only, so DIALS reads each module as its own panel. * Other: JPEG previews use a bundled encoder (libjpeg-turbo no longer needed), Rugnux prints how to cite it, and the release archives contain the HTML documentation. Reviewed-on: #92 Co-authored-by: Filip Leonarski <filip.leonarski@psi.ch>
142 lines
5.1 KiB
ReStructuredText
142 lines
5.1 KiB
ReStructuredText
Documentation
|
|
=============
|
|
|
|
.. raw:: html
|
|
|
|
<p class="jfj-lead">The manuals and reference of Jungfraujoch and Rugnux, open-source software
|
|
from the <a href="https://www.psi.ch">Paul Scherrer Institute</a> for X-ray diffraction data.
|
|
The <a href="index.html">front page</a> has the overview and the downloads; this page is the
|
|
map of the documentation.</p>
|
|
|
|
<div class="jfj-cards">
|
|
|
|
<div class="jfj-card">
|
|
<p class="jfj-card__kicker">Data processing</p>
|
|
<h2 class="jfj-card__title">Rugnux</h2>
|
|
<p class="jfj-card__text">Processes a stored macromolecular diffraction dataset, a rotation
|
|
sweep or serial stills, from the images to merged data: spot finding, indexing, integration,
|
|
scaling and merging, with the space group, cell and resolution decided from the data and a
|
|
report that says on what evidence. Given an atomic model it goes on to a refined structure and
|
|
maps: the model is placed (rigid body or molecular replacement) and refined against the merge.
|
|
One command, no parameters.</p>
|
|
<pre class="jfj-card__run"><code>rugnux <diffraction image file>
|
|
rugnux <diffraction image file> <CIF/PDB model file></code></pre>
|
|
<p class="jfj-platforms">Linux · macOS · Windows · fast on an NVIDIA GPU,
|
|
works without one</p>
|
|
<p class="jfj-card__links"><a href="RUGNUX.html">Get started</a>
|
|
<a href="RUGNUX_DOWNLOAD.html">Download</a>
|
|
<a href="RUGNUX_OVERVIEW.html">What it does</a>
|
|
<a href="RUGNUX_TUTORIAL.html">Manual</a></p>
|
|
</div>
|
|
|
|
<div class="jfj-card">
|
|
<p class="jfj-card__kicker">Desktop application</p>
|
|
<h2 class="jfj-card__title">Jungfraujoch Viewer</h2>
|
|
<p class="jfj-card__text">Shows what is in a diffraction dataset: every image with its spots,
|
|
predictions and resolution rings, per-image statistics over the sweep, grid-scan maps, and
|
|
the same processing pipeline as Rugnux, run from a settings panel on the open file. Follows a
|
|
live collection from a running Jungfraujoch broker.</p>
|
|
<p class="jfj-platforms">Linux · macOS · Windows · Qt 6</p>
|
|
<p class="jfj-card__links"><a href="JFJOCH_VIEWER.html">Get started</a>
|
|
<a href="VIEWER_DOWNLOAD.html">Download</a>
|
|
<a href="JFJOCH_VIEWER.html#a-guided-tour">Guided tour</a></p>
|
|
</div>
|
|
|
|
<div class="jfj-card">
|
|
<p class="jfj-card__kicker">Data acquisition</p>
|
|
<h2 class="jfj-card__title">Jungfraujoch</h2>
|
|
<p class="jfj-card__text">The data-acquisition and real-time analysis system for the PSI
|
|
JUNGFRAU and EIGER detectors, and for DECTRIS detectors through their control unit: an FPGA
|
|
and GPU pipeline that takes the detector's frames at full rate, analyses them on the fly,
|
|
streams them to the NXmx HDF5 writer and serves a web interface and REST API to the
|
|
beamline.</p>
|
|
<p class="jfj-platforms">Linux servers · AMD Alveo U55C FPGA · NVIDIA GPUs</p>
|
|
<p class="jfj-card__links"><a href="JUNGFRAUJOCH.html">Get started</a>
|
|
<a href="DEPLOYMENT.html">Install</a>
|
|
<a href="JFJOCH_BROKER.html">Broker</a>
|
|
<a href="JFJOCH_WRITER.html">Writer</a></p>
|
|
</div>
|
|
|
|
</div>
|
|
|
|
**Licence.** Rugnux, the viewer and the Jungfraujoch services are free software under the
|
|
:doc:`GNU General Public License v3 <LICENSE>`; the FPGA design is released under the
|
|
:doc:`CERN Open Hardware Licence v2, strongly reciprocal <FPGA_LICENSE>`. Both let anyone, in
|
|
academia or industry, use, study and modify the software and the hardware design at no charge,
|
|
commercial use included; what they ask is that a modified version which is passed on is shared
|
|
under the same terms. The released binaries bundle third-party components under GPL-compatible
|
|
licences, and the CUDA builds the NVIDIA CUDA runtime under NVIDIA's own EULA: see the
|
|
:doc:`third-party notices <THIRD_PARTY_NOTICES>`.
|
|
|
|
All pages
|
|
---------
|
|
|
|
Everything a user of Rugnux or the viewer needs comes first; the :doc:`technical reference <TECHNICAL>`
|
|
holds the algorithms, the file formats and streams, the interfaces and the FPGA design. The names
|
|
are explained in :doc:`Naming <NAMING>`, the releases in the :doc:`changelog <CHANGELOG>`, and how to
|
|
cite the software in :doc:`Publications <PUBLICATIONS>`.
|
|
|
|
.. raw:: html
|
|
|
|
<div class="jfj-sitemap">
|
|
|
|
.. toctree::
|
|
:maxdepth: 1
|
|
:caption: Rugnux
|
|
|
|
Getting started <RUGNUX>
|
|
Download <RUGNUX_DOWNLOAD>
|
|
RUGNUX_OVERVIEW
|
|
RUGNUX_INSTALL
|
|
RUGNUX_FORMATS
|
|
RUGNUX_TUTORIAL
|
|
RUGNUX_CLI
|
|
RUGNUX_REPORT
|
|
RUGNUX_INTEGRATION
|
|
RUGNUX_ADVANCED
|
|
RUGNUX_MODEL_AND_REFERENCE
|
|
Detector calibration <RUGNUX_CALIBRATION>
|
|
|
|
.. toctree::
|
|
:maxdepth: 1
|
|
:caption: Jungfraujoch Viewer
|
|
|
|
Using the viewer <JFJOCH_VIEWER>
|
|
Download <VIEWER_DOWNLOAD>
|
|
|
|
.. toctree::
|
|
:maxdepth: 1
|
|
:caption: Jungfraujoch
|
|
|
|
Overview <JUNGFRAUJOCH>
|
|
DEPLOYMENT
|
|
REPOSITORIES
|
|
RELEASE_CONTENTS
|
|
JFJOCH_BROKER
|
|
JFJOCH_WRITER
|
|
WEB_FRONTEND
|
|
MX software integration <SOFTWARE_INTEGRATION>
|
|
TOOLS
|
|
Python client <PYTHON_CLIENT>
|
|
|
|
.. toctree::
|
|
:maxdepth: 1
|
|
:caption: Reference
|
|
|
|
TECHNICAL
|
|
|
|
.. toctree::
|
|
:maxdepth: 1
|
|
:caption: Project
|
|
|
|
PUBLICATIONS
|
|
ACKNOWLEDGEMENT
|
|
LICENSE
|
|
THIRD_PARTY_NOTICES
|
|
NAMING
|
|
CHANGELOG
|
|
|
|
.. raw:: html
|
|
|
|
</div>
|